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- EMDB-61852: Cryo-EM Focused Refined Map of Human RNF213 E3 module and IpaH1.4... -

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Basic information

Entry
Database: EMDB / ID: EMD-61852
TitleCryo-EM Focused Refined Map of Human RNF213 E3 module and IpaH1.4 LRR domain
Map data
Sample
  • Complex: Human RNF213 and Shigella flexneri IpaH1.4 complex
    • Protein or peptide: E3 ubiquitin-protein ligase IpaH1.4
    • Protein or peptide: Ring finger protein 213
KeywordsRNF213 / IpaH1.4 / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


immune system process / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / toxin activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / protein ubiquitination / nucleolus / ATP hydrolysis activity ...immune system process / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / toxin activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / protein ubiquitination / nucleolus / ATP hydrolysis activity / zinc ion binding / extracellular region / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : ...E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Leucine-rich repeats, bacterial type / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Leucine-rich repeat profile. / Ring finger / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ring finger protein 213 / E3 ubiquitin-protein ligase IpaH1.4
Similarity search - Component
Biological speciesHomo sapiens (human) / Shigella flexneri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsZhang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071219 China
CitationJournal: Nat Commun / Year: 2025
Title: Shigella effector IpaH1.4 subverts host E3 ligase RNF213 to evade antibacterial immunity.
Authors: Xindi Zhou / Huijing Zhang / Yaru Wang / Danni Wang / Zhiqiao Lin / Yuchao Zhang / Yubin Tang / Jianping Liu / Yu-Feng Yao / Yixiao Zhang / Lifeng Pan /
Abstract: Ubiquitination plays vital roles in modulating pathogen-host cell interactions. RNF213, a E3 ligase, can catalyze the ubiquitination of lipopolysaccharide (LPS) and is crucial for antibacterial ...Ubiquitination plays vital roles in modulating pathogen-host cell interactions. RNF213, a E3 ligase, can catalyze the ubiquitination of lipopolysaccharide (LPS) and is crucial for antibacterial immunity in mammals. Shigella flexneri, an LPS-containing pathogenic bacterium, has developed mechanisms to evade host antibacterial defenses during infection. However, the precise strategies by which S. flexneri circumvents RNF213-mediated antibacterial immunity remain poorly understood. Here, through comprehensive biochemical, structural and cellular analyses, we reveal that the E3 effector IpaH1.4 of S. flexneri can directly target human RNF213 via a specific interaction between the IpaH1.4 LRR domain and the RING domain of RNF213, and mediate the ubiquitination and proteasomal degradation of RNF213 in cells. Furthermore, we determine the cryo-EM structure of human RNF213 and the crystal structure of the IpaH1.4 LRR/RNF213 RING complex, elucidating the molecular mechanism underlying the specific recognition of RNF213 by IpaH1.4. Finally, our cell based functional assays demonstrate that the targeting of host RNF213 by IpaH1.4 promotes S. flexneri proliferation within infected cells. In summary, our work uncovers an unprecedented strategy employed by S. flexneri to subvert the key host immune factor RNF213, thereby facilitating bacterial proliferation during invasion.
History
DepositionOct 10, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61852.png

Downloads & links

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Map

FileDownload / File: emd_61852.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 500 pix.
= 527.5 Å		1.06 Å/pix.
x 500 pix.
= 527.5 Å		1.06 Å/pix.
x 500 pix.
= 527.5 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.4929684 - 2.5424569
Average (Standard dev.)-0.00051749346 (±0.047536697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 527.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61852_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61852_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human RNF213 and Shigella flexneri IpaH1.4 complex

EntireName: Human RNF213 and Shigella flexneri IpaH1.4 complex
Components
  • Complex: Human RNF213 and Shigella flexneri IpaH1.4 complex
    • Protein or peptide: E3 ubiquitin-protein ligase IpaH1.4
    • Protein or peptide: Ring finger protein 213

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Supramolecule #1: Human RNF213 and Shigella flexneri IpaH1.4 complex

SupramoleculeName: Human RNF213 and Shigella flexneri IpaH1.4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 618 KDa

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Macromolecule #1: E3 ubiquitin-protein ligase IpaH1.4

MacromoleculeName: E3 ubiquitin-protein ligase IpaH1.4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Shigella flexneri (bacteria)
Molecular weightTheoretical: 65.28052 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGSMIKSTN IQAIGSGIMH QINNVYSLTP LSLPMELTPS MNEFYLKTWS EWEKNGTPGE QRNIAFNRLK ICLQNQEAEL NLSELDLKT LPDLPPQITT LEIRKNLLTH LPDLPPMLKV IHAQFNQLES LPALPETLEE LNAGDNKIKE LPFLPENLTH L RVHNNRLH ...String:
GPGSMIKSTN IQAIGSGIMH QINNVYSLTP LSLPMELTPS MNEFYLKTWS EWEKNGTPGE QRNIAFNRLK ICLQNQEAEL NLSELDLKT LPDLPPQITT LEIRKNLLTH LPDLPPMLKV IHAQFNQLES LPALPETLEE LNAGDNKIKE LPFLPENLTH L RVHNNRLH ILPLLPPELK LLVVSGNRLD SIPPFPDKLE GLALANNFIE QLPELPFSMN RAVLMNNNLT TLPESVLRLA QN AFVNVAG NPLSGHTMRT LQQITTGPDY SGPRIFFSMG NSATISAPEH SLADAVTAWF PENKQSDVSQ IWHAFEHEEH ANT FSAFLD RLSDTVSARN TSGFREQVAA WLEKLSASAE LRQQSFAVAA DATESCEDRV ALTWNNLRKT LLVHQASEGL FDND TGALL SLGREMFRLE ILEDIARDKV RTLHFVDEIE VYLAFQTMLA EKLQLSTAVK EMRFYGVSGV TANDLRTAEA MVRSR EENE FTDWFSLWGP WHAVLKRTEA DRWAQAEEQK YEMLENEYSQ RVADRLKASG LSGDADAERE AGAQVMRETE QQIYRQ LTD EVLALRLSEN GSNHIA

UniProtKB: E3 ubiquitin-protein ligase IpaH1.4

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Macromolecule #2: Ring finger protein 213

MacromoleculeName: Ring finger protein 213 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 553.65875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGTSTLSPG GGVTVFFHAI ISLHFPFNPD LHKVFIRGGE EFGESKWDSN ICELHYTRDL GHDRVLVEGI VCISKKHLDK YIPYKYVIY NGESFEYEFI YKHQQKKGEY VNRCLFIKSS LLGSGDWHQY YDIVYMKPHG RLQKVMNHIT DGPRKDLVKG K QIAAALML ...String:
GPGTSTLSPG GGVTVFFHAI ISLHFPFNPD LHKVFIRGGE EFGESKWDSN ICELHYTRDL GHDRVLVEGI VCISKKHLDK YIPYKYVIY NGESFEYEFI YKHQQKKGEY VNRCLFIKSS LLGSGDWHQY YDIVYMKPHG RLQKVMNHIT DGPRKDLVKG K QIAAALML DSTFSILQTW DTINLNSFFT QFEQFCFVLQ QPMIYEGQAQ LWTDLQYREK EVKRYLWQHL KKHVVPLPDG KS TDFLPVD CPVRSKLKTG LIVLFVVEKI ELLLEGSLDW LCHLLTSDAS SPDEFHRDLS HILGIPQSWR LYLVNLCQRC MDT RTYTWL GALPVLHCCM ELAPRHKDAW RQPEDTWAAL EGLSFSPFRE QMLDTSSLLQ FMREKQHLLS IDEPLFRSWF SLLP LSHLV MYMENFIEHL GRFPAHILDC LSGIYYRLPG LEQVLNTQDV QDVQNVQNIL EMLLRLLDTY RDKIPEEALS PSYLT VCLK LHEAICSSTK LLKFYELPAL SAEIVCRMIR LLSLVDSAGQ RDETGNNSVQ TVFQGTLAAT KRWLREVFTK NMLTSS GAS FTYVKEIEVW RRLVEIQFPA EHGWKESLLG DMEWRLTKEE PLSQITAYCN SCWDTKGLED SVAKTFEKCI IEAVSSA CQ SQTSILQGFS YSDLRKFGIV LSAVITKSWP RTADNFDDIL KHLLTLADVK HVFRLCGTDE KILANVTEDA KRLIAVAD S VLTKVVGDLL SGTILVGQLE LIIKHKNQFL DIWQLREKSL SPQDEQCAVE EALDWRREEL LLLKKEKRCV DSLLKMCGN VKHLIQVDFG VLAVRHSQDL SSKRLNDTVT VRLSTSSNSQ RATHYHLSSQ VQEMAGKIDL LRDSHIFQLF WREAAEPLSE PKEDQEAAE LLSEPEEESE RHILELEEVY DYLYQPSYRK FIKLHQDLKS GEVTLAEIDV IFKDFVNKYT DLDSELKIMC T VDHQDQRD WIKDRVEQIK EYHHLHQAVH AAKVILQVKE SLGLNGDFSV LNTLLNFTDN FDDFRRETLD QINQELIQAK KL LQDISEA RCKGLQALSL RKEFICWVRE ALGGINELKV FVDLASISAG ENDIDVDRVA CFHDAVQGYA SLLFKLDPSV DFS AFMKHL KKLWKALDKD QYLPRKLCDS ARNLEWLKTV NESHGSVERS SLTLATAINQ RGIYVIQAPK GGQKISPDTV LHLI LPESP GSHEESREYS LEEVKELLNK LMLMSGKKDR NNTEVERFSE VFCSVQRLSQ AFIDLHSAGN MLFRTWIAMA YCSPK QGVS LQMDFGLDLV TELKEGGDVT ELLAALCRQM EHFLDSWKRF VTQKRMEHFY LNFYTAEQLV YLSTELRKQP PSDAAL TML SFIKSNCTLR DVLRASVGCG SEAARYRMRR VMEELPLMLL SEFSLVDKLR IIMEQSMRCL PAFLPDCLDL ETLGHCL AH LAGMGGSPVE RCLPRGLQVG QPNLVVCGHS EVLPAALAVY MQTPSQPLPT YDEVLLCTPA TTFEEVALLL RRCLTLGS L GHKVYSLLFA DQLSYEVARQ AEELFHNLCT QQHREDYQLV MVCDGDWEHC YLPSAFSQHK VFVTPQAPLE AIQAYLAGH YRVPKQTLSA AAVFNDRLCV GIVASERAGV GKSLYVKRLH DKMKMQLNVK NVPLKTIRLI DPQVDESRVL GALLPFLDAQ YQKVPVLFH LDVTSSVQTG IWVFLFKLLI LQYLMDINGK MWLRNPCHLY IVEILERRTS VPSRSSSALR TRVPQFSFLD I FPKVTCRP PKEVIDMELS ALRSDTEPGM DLWEFCSETF QRPYQYLRRF NQNQDLDTFQ YQEGSVEGTP EECLQHFLFH CG VINPSWS ELRNFARFLN YQLRDCEASL FCNPSFIGDT LRGFKKFVVT FMIFMARDFA TPSLHTSDQS PGKHMVTMDG VRE EDLAPF SLRKRWESEP HPYVFFNDDH TTMTFIGFHL QPNINGSVDA ISHLTGKVIK RDVMTRDLYQ GLLLQRVPFN VDFD KLPRH KKLERLCLTL GIPQATDPDK TYELTTDNML KILAIEMRFR CGIPVIIMGE TGCGKTRLIK FLSDLRRGGT NADTI KLVK VHGGTTADMI YSRVREAENV AFANKDQHQL DTILFFDEAN TTEAISCIKE VLCDHMVDGQ PLAEDSGLHI IAACNP YRK HSEEMICRLE SAGLGYRVSM EETADRLGSI PLRQLVYRVH ALPPSLIPLV WDFGQLSDVA EKLYIQQIVQ RLVESIS LD ENGTRVITEV LCASQGFMRK TEDECSFVSL RDVERCVKVF RWFHEHSAML LAQLNAFLSK SSVSKNHTER DPVLWSLM L AIGVCYHASL EKKDSYRKAI ARFFPKPYDD SRLLLDEITR AQDLFLDGVP LRKTIAKNLA LKENVFMMVV CIELKIPLF LVGKPGSSKS LAKTIVADAM QGPAAYSDLF RSLKQVHLVS FQCSPHSTPQ GIISTFRQCA RFQQGKDLQQ YVSVVVLDEV GLAEDSPKM PLKTLHPLLE DGCIEDDPAP HKKVGFVGIS NWALDPAKMN RGIFVSRGSP NETELIESAK GICSSDILVQ D RVQGYFAS FAKAYETVCK RQDKEFFGLR DYYSLIKMVF AAAKASNRKP SPQDIAQAVL RNFSGKDDIQ ALDIFLANLP EA KCSEEVS PMQLIKQNIF GPSQKVPGGE QEDAESRYLL VLTKNYVALQ ILQQTFFEGD QQPEIIFGSG FPKDQEYTQL CRN INRVKI CMETGKMVLL LNLQNLYESL YDALNQYYVH LGGQKYVDLG LGTHRVKCRV HPNFRLIVIE EKDVVYKHFP IPLI NRLEK HYLDINTVLE KWQKSIVEEL CAWVEKFINV KAHHFQKRHK YSPSDVFIGY HSDACASVVL QVIERQGPRA LTEEL HQKV SEEAKSILLN CATPDAVVRL SAYSLGGFAA EWLSQEYFHR QRHNSFADFL QAHLHTADLE RHAIFTEITT FSRLLT SHD CEILESEVTG RAPKPTLLWL QQFDTEYSFL KEVRNCLTNT AKCKILIFQT DFEDGIRSAQ LIASAKYSVI NEINKIR EN EDRIFVYFIT KLSRVGRGTA YVGFHGGLWQ SVHIDDLRRS TLMVSDVTRL QHVTISQLFA PGDLPELGLE HRAEDGHE E AMETEASTSG EVAEVAEEAM ETESSEKVGK ETSELGGSDV SILDTTRLLR SCVQSAVGML RDQNESCTRN MRRVVLLLG LLNEDDACHA SFLRVSKMRL SVFLKKQEES QFHPLEWLAR EACNQDALQE AGTFRHTLWK RVQGAVTPLL ASMISFIDRD GNLELLTRP DTPPWARDLW MFIFSDTMLL NIPLVMNNER HKGEMAYIVV QNHMNLSENA SNNVPFSWKI KDYLEELWVQ A QYITDAEG LPKKFVDIFQ QTPLGRFLAQ LHGEPQQELL QCYLKDFILL TMRVSTEEEL KFLQMALWSC TRKLKAASEA PE EEVSLPW VHLAYQRFRS RLQNFSRILT IYPQVLHSLM EARWNHELAG CEMTLDAFAA MACTEMLTRN TLKPSPQAWL QLV KNLSMP LELICSDEHM QGSGSLAQAV IREVRAQWSR IFSTALFVEH VLLGTESRVP ELQGLVTEHV FLLDKCLREN SDVK THGPF EAVMRTLCEC KETASKTLSR FGIQPCSICL GDAKDPVCLP CDHVHCLRCL RAWFASEQMI CPYCLTALPD EFSPA VSQA HREAIEKHAR FRQMCNSFFV DLVSTICFKD NAPPEKEVIE SLLSLLFVQK GRLRDAAQRH CEHTKSLSPF NDVVDK TPV IRSVILKLLL KYSFHDVKDY IQEYLTLLKK KAFITEDKTE LYMLFINCLE DSILEKTSAY SRNDELNHLE EEGRFLK AY SPASRGREPA NEASVEYLQE VARIRLCLDR AADFLSEPEG GPEMAKEKQC YLQQVKQFCI RVENDWHRVY LVRKLSSQ R GMEFVQGLSK PGRPHQWVFP KDVVKQQGLR QDHPGQMDRY LVYGDEYKAL RDAVAKAVLE CKPLGIKTAL KACKTPQSQ QSAYFLLTLF REVAILYRSH NASLHPTPEQ CEAVSKFIGE CKILSPPDIS RFATSLVDNS VPLLRAGPSD SNLDGTVTEM AIHAAAVLL CGQNELLEPL KNLAFSPATM AHAFLPTMPE DLLAQARRWK GLERVHWYTC PNGHPCSVGE CGRPMEQSIC I DCHAPIGG IDHKPRDGFH LVKDKADRTQ TGHVLGNPQR RDVVTCDRGL PPVVFLLIRL LTHLALLLGA SQSSQALINI IK PPVRDPK GFLQQHILKD LEQLAKMLGH SADETIGVVH LVLRRLLQEQ HQLSSRRLLN FDTELSTKEM RNNWEKEIAA VIS PELEHL DKTLPTMNNL ISQDKRISSN PVAKIIYGDP VTFLPHLPRK SVVHCSKIWS CRKRITVEYL QHIVEQKNGK ERVP ILWHF LQKEAELRLV KFLPEILALQ RDLVKQFQNV QQVEYSSIRG FLSKHSSDGL RQLLHNRITV FLSTWNKLRR SLETN GEIN LPKDYCSTDL DLDTEFEILL PRRRGLGLCA TALVSYLIRL HNEIVYAVEK LSKENNSYSV DAAEVTELHV ISYEVE RDL TPLILSNCQY QVEEGRETVQ EFDLEKIQRQ IVSRFLQGKP RLSLKGIPTL VYRHDWNYEH LFMDIKNKMA QDSLPSS VI SAISGQLQSY SDACEVLSVV EVTLGFLSTA GGDPNMQLNV YTQDILQMGD QTIHVLKALN RCQLKHTIAL WQFLSAHK S EQLLRLHKEP FGEISSRYKA DLSPENAKLL STFLNQTGLD AFLLELHEMI ILKLKNPQTQ TEERFRPQWS LRDTLVSYM QTKESEILPE MASQFPEEIL LASCVSVWKT AAVLKWNREM R

UniProtKB: Ring finger protein 213

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137886
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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